Brooks Automation Inc. said it will cut 100 jobs, or 6 percent of its workforce, as it looks to “achieve cost synergies” following an acquisition and to improve profitability in a tough economic environment. The Chelmsford company, which provides automation, vacuum, and instrumentation products for such markets as the semiconductor industry, said 29 of the jobs being be cut are in Massachusetts. Brooks disclosed details of its restructuring plan in a regulatory filing.